Past Comes To Present
by mortalinstrumentsgurl1
Summary: Sebastian is dead or will he be? Clary must choose between two boys that she loves but when a new evil comes upon them, everything will go into disaster. New forms of creatures have been made by the Mother of Warlock's, Lilith. Two strong predators into one. Will the Hybrids distinguish all Nephilim race, making all the events in the past haunt the present.
1. I Pick Him, I Think

**Full summary: Sebastian is dead and gone but is he? When Lilith makes Vampire Werewolf Hybrids will they wipe out the whole race of all Nephilim and bring back her son? When one Downworlder murder becomes one hundred mundane murders. But Clary has more than that problem. She must choose from Raphael's saying that she has one week to choose between him or Jace. Will she choose the one her friends want or what her heart wants? Will the Nephilim Race end and become the past or continue on into the future? Who will Clary choose and what will happen when the past events come to haunt the present?**

***So i hope you like the sequel to my story I Love Him, I Love Him Not. If you haven't read it, go check it out and review what you think about it. SO this is mostly with Clary and Raphael will be in the next chapter and the rest. But i hope you like this.**

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Clary POV

She woke up from the sunlight hitting her eyes. It has been four days since her encounter with Raphael.

_One week to make up my mind,_ she said in her mind. She still didn't know who to choose. She had three more days till she had to tell him her answer. She hadn't seen him ever since.

Clary stretched and got out of bed and did her daily routine.

Once finished, she went to the kitchen, where there was a note on the fridge.

_Be back soon, at a Clave meeting,_

_Mom and Luke_

Clary sighed and put the note on the table, where there was a cup of coffee and a blueberry muffin waiting for her. She took the coffee and out on a jacket. She left her house and started to make her way to Simon's.

_I like the both of them but I can't them both. I have to choose. Jace loved me from the start and is nice and gentle and caring and loving but Raphael can sometimes be like that but it would only make me drown in him. _

She sighed. She went up the step and knocked. She played with the two rings Jace and Raphael gave her. A ring and a snowflake. Two complete different things that meant so much.

Simon opened the door and said, "Hey."

She smiled. She went inside and to his room.

""What's up?" he asked.

"Nothing much," lie. She had a ton of things to do and explain.

She looked at the tv in his room. He was playing the new Assassin's Creed game.

"I have a totally, weird question to ask you," Clary said, sitting on his bed.

"What is it?" he said, getting back to his game.

"You know that Isabelle and Maia like you. So if you had to choose one, who would it be and why?"

He looked at her with a confused face,

"What type of question is that?" he asked.

"Oh, just answer the question," she said.

"I don't know. There both awesome and beautiful girls that shouldn't be messed with but very fun to hang with. Isabelle is feisty and isn't scared when she needs to be and takes care of others like they're family members. But Maia, she different and the complete opposite of Isabelle. She doesn't treat me like I'm a Downworlder, just a complete ordinary human being. But I don't know who to choose."

Clary groaned. That didn't really help her at all.

"Are you asking me this to choose between Jace and Raphael?" he asked, grinning.

"Maybe," she said too quickly.

"Clary, no offense, but why do you like Raphael?" Simon asked, putting the controller down and sitting next to her on the bed.

"Well, he has this pull on me and he's very nice to me and likes me," Clary said.

"Okay, but he almost killed you when you first met him. He tricked you and Jace, remember?" Simon said. She did remember. He was kind to her when he helped her down the grate but that was just an act.

"Yeah, but he seems different," Clary said,

"To you maybe but not for the rest of us," Simon said.

Clary scoffed.

"Some help you are," she said and got up, throwing her empty coffee cup into the small trash bin.

"Clary, I'm just being honest. Yeah, Raphael may have his ups and downs, but he isn't the vampire you would want to mess with. What if you two have a fight? He could hurt you or do something far more worse, Clary. He may act like he likes you but the monster he is in the inside will come out and hurt you," Simon said to her.

Clary didn't know what to say. Simon was right and maybe wrong. Was she so blinded by love and lust to see the meaning about him from someone so close to her?

"You may be right, so you're saying that I'm better off with Jace than Raphael?" she asked, making him confirm her final choice.

He nodded.

"Okay," she said. She stayed at Simon's for a few hours but had to go.

_So it's Jace,_ she said in her mind but her heart sunk.

She was, _sad._ For Raphael. So, she might like him, a lot. But sad for a man that could kill her in one strike, _or bite, _her conscious added.

But she knew Jace wouldn't do that to her, Raphael had a fifty – fifty chance on doing so.

Jace, she had to go along with her choice. Many of her friends and family have told her or hinted her to stay away from Raphael and be with Jace.

_But, Jace has to be the right choice. Think about the consequences if you're going to be with Raphael. A dead or undead life. I want to live my life._

Clary sighed. Jace, that's it.

How would Raphael react? He would be definitely angry and outraged at her but she wanted what the heart wanted.

_Or what my friends and family wanted._

She wanted to kick the living shit out of her conscious arguing with her. She didn't even realize that she had walked to the Institute.

_I should tell Jace_.

She walked up the step and put her hand on it.

She was going to say the first word but the doors opened with a loud bang. She walked in and took the elevator up. She looked in the mirror. She was flushed from the coldness and her hair was frizzed.

What could those two boys see in her? She was just plain: having a flat chest, pale skin, freckles, and just being short.

She wasn't anything special. She was just Clary.

She stepped out the elevator after it stopped. She saw Church lying on his stomach.

"Hey Church, where's Jace?" she asked the blue Persian cat. The cat meowed and got up. He led her to the library.

She found Jace in one of the arm chairs, reading a book. The fire was ablaze and the light that casted from it formed on his figure, dancing around. As if sensing her, he looked at her.

"Hey," he said, setting the book aside.

"Was I interrupting something?" she asked him, entering the library and standing in front of him. He looked up at her.

"Nothing, just reading," he said.

She just smiled, awkwardly.

"Is there something you need to tell me?" he asked, cocking an eyebrow up and she had to roll her eyes. She still couldn't do that.

"Yeah, I- ," she started but didn't finish because Marsye, Alec, Isabelle, and Robert came in.

"Clary, thank god you're here. I'll call your mother to tell her you're here," Marsye said and taking out her cell phone.

"What's wrong," Jace asked, getting up.

"There's been a murder or what seems like a murder with one of the werewolves in Luke's pack. A guy named Aaron. We found his body near an alley. He looked beaten up but there was a needle next to him and it was broken. But he died from a silver blade," Isabelle explained.

"So what's the big deal?" Jace asked, not seeming surprised about what she told him.

"The big deal Jace," Alec started, "is that Aaron was changing. He's paler than he was and has black eyes. Not like a werewolf that has glowing yellow eyes."

"Those descriptions sound like a vampire," Clary said.

"Exactly. Now, we're trying to figure out why he's like that," Robert said. Marsye came back.

"She said stay with Jace, Isabelle, or Alec."

"Okay," Clary said.

How's it possible that Werewolf would look like a Vampire?

"We're going to need to inform all the Downworlders," Marsye said.

"Yeah, Alec, go tell Magnus what's happened. Isabelle, tell the fey. Jace, go to Raphael's clan and tell them what has happened and try not to get into another fight with him. Clary, stay here. I have already told Jocelyn to inform Luke and his pack about it. Go after we contact them but Alec go and try not to get into any trouble," Marsye ordered and Alec left.

The other two teenagers waited till their parents contacted with the two remaining Downworlders. She could see Jace's jaw contract and tense. He really didn't want to go to the Dumort.

Clary grabbed her phone and texted Simon what had happened.

He replied, _Jesus, who could've done it. But for the most parts, it didn't hurt anyone of you._

_Be careful and stay safe_, she texted back and put the phone back into her pocket. She had realized that Isabelle was gone.

She took a breath and let it out slowly.

"Don't worry Clary, I won't let whoever did that, hurt you," Jace said. She smiled at his protectiveness.

"Thanks," she said.

"What was it that you wanted to tell me?" she asked. Before she could say anything, Marsye interrupted.

"Jace, it's time for you to go," she said.

"Sorry again for the interruptions," he said and was coming in but stopped himself and left.

_He was going to kiss me, I know it_, she thought.

She took another breath. But she couldn't think straight. She was kinda terrified at the thing or person that had done something terrible to the Werewolf boy.

She sat down, trying to calm herself down at what was going to happen later in the future.

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**So it's really not that long but it's late at night and I am tired. But review and I hope you like this story. **


	2. She's Dying

Jace POV

He didn't want to go to the Dumont right now. He was still pissed at the Leech for taking Clary's virginity away and that he had a fond for her now.

The morning light hit his back; the sun may be out but it was still cold from the December air. It was only the fifth and it was cold as hell.

He had reached the Spanish Harlem. He could see the hotel in the distance. He gave a breath and made his way there. It wasn't a long walk, just under ten, maybe; Jace just made the walk longer by slowing down his pace. He could feel his anger bubble up inside of him the closer he got to the hotel.

He made his way to the alley way. He stood in the mouth of it, remembering the moment he and Clary were going to break in, then, Raphael showed up.

He shook his head and went over to the grate. He opened it, it was loosened more.

He dropped down and waiting there, out of the little lights that came through the grate, was Raphael.

"Your step mother called. What do you want?" he asked. Jace couldn't see his face since he was in the shadows.

"There's been a Downworld murder, a werewolf. He was beaten and killed by a silver blade. But he was changing, we guess into one of you," Jace explained and he caught a glimpse of Raphael's face, it looked surprised. That was the most expression he ever saw in this guy.

"He was transforming into a Vampire?" Raphael asked. Jace nodded.

"Marsye wants me to tell you that to keep your clan safe and always stay in a group," Jace said.

"Thanks, Angel Boy. You can go now," Raphael said and turned to leave. Jace only stood there. On his way to the hotel, he imagined Raphael asking questions on what has happened and arguing and being hard to tell him; but it was the opposite.

Jace went with it and helped himself up the hole and put the grate over the hole and walked back to the Institute.

Raphael POV

_He was transforming into a Vampire,_ Raphael was in thought. He remembered Jeremy telling him that the creature was a Hybrid and was half Vampire, half Werewolf.

_He also told me it could be injected into them._

He hadn't heard Jeremy for four days now and he had not seen Clary for that long either. He made a plan to go with Elliot to see Jeremy.

He went to his room and grabbed his cell phone. He called Jeremy, nothing. He called Elliot.

"Hey," he answered.

"When the sun goes down we're going to see someone," Raphael ordered.

"Okay but where to?" Elliot asked.

"Blackwell's Island," Raphael answered and hung up.

He sat on his bed and wiped his palms against his face. He was having a hard time this month.

Jace was in the way with his relationship with Clary, Jeremy won't pick up so he could ask him if there was any progress, the Hybrid was created, and maybe there are more Hybrids being created.

But he was mostly concentrating on his relationship with Clary. Three more days till she tells him who she would choose. He hadn't talked to her or seen her since their last encounter.

He sighed and looked at the clock. It was only ten in the morning. He lay back, looking at the ceiling. Just thinking what to do. But he felt himself drift away to sleep and everything went black.

Clary POV

She walked randomly around the Institute, not knowing what to do. She had no one to talk to and she couldn't leave yet. She stopped and leaned against the wall. She slid down and sighed.

_Should I tell Raphael now or when he sees me?_

She was scared on how he would react to her decision.

_But would I give up Raphael?_

She was in love with Raphael. She was in love with Jace. She couldn't have both of them, only one.

Was Jace a good choice for her? Was Raphael?

She groaned. _Why did this have to be so hard? _She asked herself.

"Hey," someone said, she looked up and saw Jace.

"Hey," she said.

"You okay?" he asked her, sliding down next to her.

"I don't know," she admitted. She felt trapped on the inside like a fly in a venus fly trap.

"What's on your mind then, let's see if I can help," Jace offered. He was so nice and kind to her, why wouldn't he be the right guy to be with?

"I don't know if you'll be the right person to help me with this situation," she said, looking at his golden eyes.

"What's it about?"

"Well, it's about my love life. If I should be with you or Raphael," she said, staring at something that wasn't his eyes.

"Well, what do you have to say about the both of us?" he asked, hesitation twinkling in his voice.

"You, you're so nice and caring and every girl's dream to be with and I fell in love with you because of the way you are. Raphael is just rude and cocky but he has a nice and caring side too. And I guess I fell in love with the way he is too," Clary said, deep in thought.

She heard Jace sigh, it must have been awkward for him to have this conversation about him and Raphael.

"I'm just going to tell you this Clary, it's your decision and life. You choose it, you make your future," Jace said. She finally looked at him.

"But everyone tells me to be with you and stay away from Raphael, they give me hints to do it, it just makes me confused I what I want. If I want what my friends want to make them happy or what I want to make me happy," she said, tears were starting to trickle down her face.

"Clary, you're a smart girl. I want you to be happy with anyone you choose. You choose who you want, what your heart wants. Don't make your friends choose your future, they have their own life," Jace said to her, he wiped the tears away.

"I don't know what to do," she cried and he hugged her. She cried into his shoulder; Jace rubbing circles on her back.

"I don't know if this is a smart idea, but you should talk to Raphael about it, if you want to," Jace said, pulling back to look at her.

"I think that's somewhat a good idea," she said.

"Do you want me to come with you?" he asked. She didn't think about what to tell him but she nodded.

"Okay," he said softly and hugged her again.

_Maybe it was the wrong thing to say if he and Raphael see each other again._

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It has been some hours since the murder has been discovered. It was almost two when Isabelle and Alec came back, the Downworlders understood and Maryse even got a phone call Luke.

Maryse had informed Clary that she could spend the night at the Institute.

She had spent her time with Jace, doing friend stuff. They even had fun.

Jace and her agreed to go see Raphael tonight.

"So, what are you going to say to Raphael?" Jace asked. The two of them were in the kitchen, both hungry.

"I don't know, what should I say?" she asked Jace, sitting in one of the stools. He looked through the fridge and took out a bowl that had cut up fruit in it. He grabbed two forks and handed her one. He peeled off the plastic wrap off and threw it away.

"Tell him how you feel and whatever you have to say to him," Jace said and ate a piece of fruit.

"Last time I told him how I feel he abandoned me," Clary muttered and it didn't seem that Jace heard her say anything.

It was silent between the two for a while.

"I'm sorry," she blurted and he looked at her.

"For what?" he seemed confused.

"For cheating behind your back. I didn't mean to," she said softly.

"It's okay," he said.

"No it's not. I hurt you, Jace," she said.

"I may have been hurt but I still know that you love me," he said.

"Yeah," she said and sighed.

The kitchen door opened and Alec showed up with Magnus at his side.

"Mom wants all of us in the library," he said.

"For what?" Jace asked him.

Alec's blue eyes were weary and tired. Has he even slept? Maybe not, ever since Max died, Alec had seemed more distant but not that distant.

"Don't know, she just needs to see all of us," he said and left with Magnus trailing behind him. The two looked at each other and followed the two.

Once they got into the library, they saw something so gruesome that Clary thought she was going to faint or throw up.

Her mother, with her head on Maryse's lap. Her eyes were closed and she was pale as ever.

"Mom," Clary said.

She saw Luke, he looked tired and had scratch marks on him that weren't healing.

"What happened?" Jace asked.

"We were attacked at home. We tried to get rid of them but Jocelyn she got hurt. They pierced her with a Demon Blade," Luke looked at Clary.

"She's dying and if we can't heal her then she won't wake up," Luke said.

Clary was so horrified and scared. She fainted and Jace caught her. Tears running down too.

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**I hope you like this chapter and Happy New Years! I hope you guys had a wonderful Christmas and New Years. So my winter break is almost over and i will try to get a chapter up before it ends and i know this one isn't long but I have been having trouble sleeping and i don't know why so I'll try to make next chapter longer and reviews! :D**


	3. I Need To See You

Raphael POV

It was sunset and Raphael and Elliot made their way to Blackwell's Island.

"So, why are we going here?" Elliot asked, his dreads swaying.

"Seeing a friend," Raphael said simply.

"Look, ever since our Change happened, you can't be distant from me. We're still friends," he said and Raphael looked at him.

"I know," Raphael said and looked ahead of him.

"I'm serious," he said and stopped, making Raphael stop with him.

"Elliot," Raphael said but he shook his head.

"Raphael, I know you're the clan leader, we can still be friends and all that we were before. You're like a brother," he said.

Raphael just looked at him. Elliot and him were best friends before the Change and they would always do stuff together. Even when they Changed, they still were friends but distanced.

"I know we are and we will always be," Raphael said and Elliot smiled. They started walking again.

"Now, are you going to tell me why you like the redhead?"

Jace POV

He had put Clary in his bed. She was tensed. It was too much for her that knowing her mother might die. He swept a piece off hair off her face. He missed her, a lot. All because of Raphael. Jace couldn't stand the guy at all. He would kill him if he could.

He sighed. If it weren't for him, his relationship with Clary could've been more passionate and lustful, but no.

He heard her stir and looked at her. She opened her eyes and looked at him.

"Are you feeling okay?" he asked her and she sat up with his assistance. She looked at up at him and he noticed how close they were. He couldn't help but close the distance. Their lips touched and he felt the shock but she pushed him away. He looked hurt.

"Clary," he started but she shook her head, got up, and ran out the room.

Clary POV

She ran, the kiss with Jace seemed wrong to her. She went down the elevator and out the Institute. She had a feeling in her stomach. She had to see Raphael. She just needed to. The sun has set, she was passed out for a long time. She wanted to go to the Dumort but she was tired of running so she took a break. It was cold and she didn't bother putting on a jacket when she left. She out her face in her hands.

Why was this so hard? _Why can't I have a normal life?_ She asked herself. She sat on a bench and huffed for air.

She took her phone from her pocket. It was six thirty. She went to her contacts and pressed call for Raphael.

It rang twice till he picked up.

"Hello," he said.

"I need to talk to you," she came out.

"I'm busy right now, precious," he said.

"Well, whenever you're available, I have to talk to you," she said.

"Okay," Raphael answered.

It was silent till she hung up. She didn't know why but she started crying. All her emotions coming up for both boys she loved very much.

Raphael POV

Clary had called him and it seemed like she was desperate to talk to him. He put his phone up and the two arrived at the abandoned hospital. They entered and the scent of blood hit them. They looked at each other and followed the smell. It was from the basement, Raphael had last visited Jeremy.

When they reached the door, it was slightly opened. Then they saw Jeremy, lying in his own pool of blood on the ground. They made their way to the dead body.

"Who do you think did this?" Elliot asked Raphael, who both squatted down and looked at Jeremy.

"I don't know but it has to be that Hybrid," Raphael said, looking at the open cage.

"What?"

"Last time I saw Jeremy, there was a human created Hybrid in there," Raphael pointed at the cage.

"Well, now where did it go?" Elliot asked, looking at the cage.

"Well, that's an answer to look for," Raphael said. And they looked at each other, knowing what they would find, they wouldn't like.

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**Sorry that it isnt long but it's late at night and i found out that i have a little sleeping disorder and i hope i get better and i hope you like this small chapter.**

**:D I think shout outs are going to be in the next chapter**


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